For those who use this procedure or have carried out digestion with proteolytic
enzymes in solution, the resulting peptides can be identified using UCSF MS
Fit

Once a potential match has been made, MS Digest can be used to predict
all potential peptides including user-specified posttranslational modifications. UCSF MS Digest

2D-proteomics databases are available for many cell types and organs/tissues from several
species as well as subcellular fractions. These are frequently annotated
with regard to spot identification. The EXPASY site contains links to
these databases as well as other useful programs and software for mass
spectrometry http://www.expasy.org/ch2d/